6SUA

Structure of the high affinity engineered lipocalin C1B12 in complex with the mouse CD98 heavy chain ectodomain


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6I9Q6I9Q, 6S8V
experimental modelPDB 6S8V6I9Q, 6S8V

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529312 %(w/v) PEG8000, 0.2 M Li2SO4
Crystal Properties
Matthews coefficientSolvent content
2.7154.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 105.039α = 90
b = 107.737β = 90
c = 133.872γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2M2018-03-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.9184BESSY14.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.7534.7199.10.1970.2050.99615.3613.1983985642.73
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.752.8596.61.0791.1280.7692.4511.718

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6I9Q, 6S8V2.7534.7137895196199.090.22220.21970.2709RANDOM43.758
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-0.85-3.224.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.391
r_dihedral_angle_4_deg14.819
r_dihedral_angle_3_deg14.552
r_dihedral_angle_1_deg6.297
r_angle_refined_deg1.182
r_angle_other_deg1.068
r_chiral_restr0.039
r_gen_planes_refined0.003
r_bond_refined_d0.002
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.391
r_dihedral_angle_4_deg14.819
r_dihedral_angle_3_deg14.552
r_dihedral_angle_1_deg6.297
r_angle_refined_deg1.182
r_angle_other_deg1.068
r_chiral_restr0.039
r_gen_planes_refined0.003
r_bond_refined_d0.002
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9424
Nucleic Acid Atoms
Solvent Atoms146
Heterogen Atoms60

Software

Software
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing